---
directories:
    work_dir: /usr/local/www/data/private/Dalbergia/odorifera
    from_annot_dir: 10.5524/100760
    from_genome_dir: 10.5524/100760
prefixes:
    from_annot_prefix: "Dod." 
    from_genome_prefix: "Dod."
collection_info:
    genus: Dalbergia
    species: odorifera
    scientific_name_abbrev: dalod
    coll_genotype: SKLTGB
    gnm_ver: gnm1
    ann_ver: ann1
    genome_key: BB3V
    annot_key: R67B
readme_info:
    provenance: "The files in this directory originated from GigaDB, dataset 100760 submitted by the Daping Xu lab, State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou China. The GigaDB source is considered the primary repository and authoritative; files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and SoyBase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the LegumeInfo and SoyBase projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please respect any usage restrictions in the present and original repositories, and cite the data appropriately."
    source: "http://gigadb.org/dataset/100760"
    synopsis_genome: Genome assembly for Dalbergia odorifera, isolate SKLTGB
    synopsis_annot: Annotation for Dalbergia odorifera, isolate SKLTGB
    taxid: "499988"
    genotype: SKLTGB
    description_genome: "This assembly is based on Illumina short reads, PacBio long reads, Hi-C data, and 10x Genomics linked-reads"
    chromosome_prefix: chr
    supercontig_prefix: Scaffold
    description_annot: "This annotation was produced by the State Key Laboratory of Tree Genetics and Breeding, using a combination of homologous comparison, ab initio prediction, and RNA-seq–based annotation"
    bioproject: "PRJNA613774"
    sraproject: 
    dataset_doi_genome: 10.5524/100760
    dataset_doi_annot: 10.5524/100760
    genbank_accession: 
    original_file_creation_date: 2020-07-01
    local_file_creation_date: 2023-08-28
    dataset_release_date: 2023-09-01
    contributors: Hong Z; Li J; Liu X; Lian J; Zhang N; Yang Z; Niu Y; Cui Z; Xu D
    publication_doi: 10.1093/gigascience/giaa084
    citation: "Hong Z, Li J, Liu X, Lian J, Zhang N, Yang Z, Niu Y, Cui Z, Xu D. The chromosome-level draft genome of Dalbergia odorifera. Gigascience. 2020 Aug 1;9(8):giaa084. doi: 10.1093/gigascience/giaa084. PMID: 32808664; PMCID: PMC7433187."
    publication_title: "The chromosome-level draft genome of Dalbergia odorifera"
    data_curators: Steven Cannon
    public_access_level: public
    license: open
    keywords: "Chinese rosewood, Dalbergia odorifera"
from_to_genome:
  - 
    from: genome.chr.fa.gz
    to: genome_main.fna
    description: "Primary genome assembly"
original_readme_and_usage:
from_to_annot_as_is:
from_to_genome_as_is:
from_to_cds_mrna:
  - 
    from: cds.fa.gz
    to: cds.fna
    description: "cds sequences"
from_to_protein:
  - 
    from: pep.fa.gz
    to: protein.faa
    description: "Protein sequences"
from_to_gff:
  - 
    from: chr.gff3.gz
    to: gene_models_main.gff3
    description: "Gene models - main"